Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

cell proliferation > PTM > Flashcards

PTM Flashcards

1
Q

what do cells need to do to maintain homeostasis

A

to detect changes in their environment and respond accordingly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

how quick are the response to homeostatic changes

A

~ms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what can dynamic-rapid responses not be achieved using

A

gene transcriptional regulation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are PTMs suitable for

A

relaying rapid messages within the cell as they are dynamic, quick and reversible

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

are PTMs reversible

A

yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is the definition of PTM

A

post-translational modification (the modifications proteins undergo after translation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are PTMs and what are they introduced to

A

covalent additions to amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what do PTMs do to the modified residue

A

change the physicochemical properties

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are examples of small group PTMs

A

phosphate or acetyls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what are examples of large polypeptide PTMs

A

Ubiquitin or SUMO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

how many PTMs have been identified

A

over 200

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are some PTM examples

A

phosphorylation, acetylation, ubiquitination, SUMOylation and methylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are the writers and erasers of phosphorylation

A

kinase and phosphatase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are the writers and erasers of ubiquitination

A

ubiquitin E3 ligase and deubiquitinase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what are the writers and erasers of SUMOylation

A

SUMO E3 ligase and deSUMOylase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what are the writers and erasers of acetylation

A

acetyltransferase and deacetylase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what are the writers and erasers of methylation

A

methyltransferases and demethylases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

how many kinds of kinase are there

A

more than 500

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

how many kinds of phosphatases are there

A

200

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

how do kinases work

A

bind to an ATP molecule and takes up the gamma phosphate, gamma then can bind to the substrate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what are the characteristics of phosphate groups

A
  • large and bulky
  • have a specific “shape”
  • negatively charged (up to 2 negative charges) at a neutral pH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what happens when you add a phosphate group to a protein

A

it alters the shape and charge of the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what can PTMs induce

A

conformational changes and promote interaction with proteins that have affinity for modified residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what are the 2 types of conformational change

A
  • long-range disruption
  • long-range ordering
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what can PTMs modulate

A
  • activity (either promote or inhibit)
  • localisation
  • stability
  • complex formation
  • selectivity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what is an example of PTMs modulating activity

A

kinase activity by phosphorylation of its activation loop

27
Q

what is an example of PTMs modulating localisation

A

by modifying/masking Nuclear Localisation SIgnals

28
Q

what is an example of PTMs modulating stability

A

ubiquitin-mediated proteasomal degradation

29
Q

what is an example of PTMs modulating complex formation

A

the formation of docking sites

30
Q

what is an example of PTMs modulating selectivity

A

promoter specificity mediated by phosphorylation (eg p53)

31
Q

can a protein be modified by multiple PTMs

A

yes, they can be modified by more than one type of PTM OR modified by the same PTM at different residues

32
Q

what happens when PTMs are seperated in time

A

they can occur sequentially on a single site in a protein

33
Q

what happens in positive crosstalk

A

one PTM serves as a signal for the addition or removal of a second PTM

34
Q

what happens in negative crosstalk

A

it can be a direct competition for modification of a single residue in a protein, or indirectly by masking the recognition site for a second PTM

35
Q

how can you measure PTMs in cells

A
  • antibodies that recognise specific PTMs
  • mass spectrometry (measures the mass-to-charge ratio of one or more molecules present in a sample)
36
Q

how are modified-specific antibodies generated

A

using a modified peptide as an antigen

37
Q

how do modified-specific antibodies work

A

antibody recognises both the modified group AND parts of the peptide surrounding the modified site

38
Q

what are modified-specific antibodies usually used for analysiing

A

phosphorylation, acetylation and methylation

39
Q

what are the advantages of modified-specific antibodies

A
  • cheap
  • can provide quantitative information
  • can identify subtle differences
  • very sensitive
  • highly specific
40
Q

what are the disadvantages of modified-specific antibodies

A
  • only works if you already have information about where your protein is modified and the type of modification
  • there are not antibodies avaliable for each modified protein
  • producing new antibodies is time consuming, expensive and not always successful
41
Q

what is mass specotrometry

A

an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. these spectra are used to elucidate the chemical structures, such as peptides and other chemical compounds

42
Q

what is the order of a mass spectrometry reading

A

sample - gass/liquid chromatography (seperation step) - ionisation interface - mass spectrometer (measures mass)

43
Q

what do peaks in a mass spectrometer reading show

A

that phosphorylation has occured

44
Q

what can mass spectrometers not read

A

they cannot determine between AA numbers - if there are 2 serines next to each other it cant determine which is which

45
Q

what are the advantages of mass spectrometry

A
  • provides unbiased/untargeted information
  • it can differentiate very similar proteins/isoforms (ie substitution in a single AA)
  • it can generate a huge amount of information (eg it can identify different modifications in hundreds of proteins in the same sample)
  • it can be quantitative (allows to make clear differentiations between 2 species (eg KO and WT))
46
Q

what are the disadvantages of mass spectrometry

A
  • can be expensive and time consuming
  • often difficult to pinpoint the position of the phosphorylation site with single AA residues
  • very abundant proteins will mask low abundance proteins (eg if hair falls in, all that it will show is keratin)
  • you need the expertise
47
Q

what are protein kinases

A

enzymes that catalyse the transfer of phosphate from ATP to their substrate

48
Q

are kinases specific

A

yes

49
Q

are phosphatases specific

A

no, they are “promiscious”

50
Q

how many genes code for kinases in the human genome

A

538 (2% of total genes)

51
Q

which human kinases are most abundant

A

ser/Thr or Tyr kinases

52
Q

what can kinases be clustered into

A

groups, families and sub-families of increasing sequence similarity and biochemical function

53
Q

what is the structure of protein kinases

A

all have a conserved core with the same basic 3D organisation, comprising of 2 lobes with the active site, where the ATP binds, in a cleft between the lobes

54
Q

what do tyrosine kinase signalling pathways control

A

the most fundamental processes of the cell (such as cell proliferation, differentiation, motility and cell death / survival)

55
Q

what happens to tyrosine kinases in tumour cells

A

they are often deregulated due to hyper-activating mutations, amplification/overexpression or loss of negative regulation

56
Q

what do aberrant constitutive phosphorylation sustain

A

oncogenic signal transduction pathways

57
Q

how many of known oncogenes are protein kinases

A

approx half

58
Q

how many oncology drugs that target kinases have been approved

A

around 40

59
Q

what is the major difference between non-covalent and covalent inhibitors

A

non-covalent inhibitors are reversible whereas covalent inhibitors are irreversible

60
Q

what are the characteristics of type I protein kinase inhibitors

A
  • reversible
  • binds to ATP site
  • is ATP-competitive
  • low selectivity
61
Q

what are the characteristics of type II protein kinase inhibitors

A
  • reversible
  • binds to ATP site and DFG pocket
  • not ATP-competitive
  • high selectivity
62
Q

what are the characteristics of type III protein kinase inhibitors

A
  • reversible
  • allosteric binding (outside of ATP-binding site)
  • not ATP-competitive
  • very high selectivity
63
Q

what are the characteristics of type IV protein kinase inhibitors

A
  • reversible
  • allosteric binding (substrate binding domain)
  • not ATP-competitive
  • very high selectivity
64
Q

what are the characteristics of covalent inhibitors

A
  • irreversible
  • binds to ATP site
  • not ATP-competitive
  • low selectivity

cell proliferation (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions